Literature DB >> 25349911

The big data challenges of connectomics.

Jeff W Lichtman1, Hanspeter Pfister2, Nir Shavit3.   

Abstract

The structure of the nervous system is extraordinarily complicated because individual neurons are interconnected to hundreds or even thousands of other cells in networks that can extend over large volumes. Mapping such networks at the level of synaptic connections, a field called connectomics, began in the 1970s with a the study of the small nervous system of a worm and has recently garnered general interest thanks to technical and computational advances that automate the collection of electron-microscopy data and offer the possibility of mapping even large mammalian brains. However, modern connectomics produces 'big data', unprecedented quantities of digital information at unprecedented rates, and will require, as with genomics at the time, breakthrough algorithmic and computational solutions. Here we describe some of the key difficulties that may arise and provide suggestions for managing them.

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Year:  2014        PMID: 25349911      PMCID: PMC4412267          DOI: 10.1038/nn.3837

Source DB:  PubMed          Journal:  Nat Neurosci        ISSN: 1097-6256            Impact factor:   24.884


  20 in total

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4.  Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling.

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Review 5.  Cellular-resolution connectomics: challenges of dense neural circuit reconstruction.

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Journal:  Nat Methods       Date:  2013-06       Impact factor: 28.547

Review 6.  Ome sweet ome: what can the genome tell us about the connectome?

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Journal:  Curr Opin Neurobiol       Date:  2008-06       Impact factor: 6.627

Review 7.  Toward large-scale connectome reconstructions.

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Journal:  Curr Opin Neurobiol       Date:  2014-03-02       Impact factor: 6.627

8.  Network anatomy and in vivo physiology of visual cortical neurons.

Authors:  Davi D Bock; Wei-Chung Allen Lee; Aaron M Kerlin; Mark L Andermann; Greg Hood; Arthur W Wetzel; Sergey Yurgenson; Edward R Soucy; Hyon Suk Kim; R Clay Reid
Journal:  Nature       Date:  2011-03-10       Impact factor: 49.962

9.  Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure.

Authors:  Winfried Denk; Heinz Horstmann
Journal:  PLoS Biol       Date:  2004-10-19       Impact factor: 8.029

10.  Space-time wiring specificity supports direction selectivity in the retina.

Authors:  Jinseop S Kim; Matthew J Greene; Aleksandar Zlateski; Kisuk Lee; Mark Richardson; Srinivas C Turaga; Michael Purcaro; Matthew Balkam; Amy Robinson; Bardia F Behabadi; Michael Campos; Winfried Denk; H Sebastian Seung
Journal:  Nature       Date:  2014-05-04       Impact factor: 49.962

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  48 in total

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Authors:  Erin D Bigler
Journal:  Neuropsychol Rev       Date:  2015-08-18       Impact factor: 7.444

2.  Teaching 'big data' analysis to young immunologists.

Authors:  Joachim L Schultze
Journal:  Nat Immunol       Date:  2015-09       Impact factor: 25.606

Review 3.  Annual Research Review: Discovery science strategies in studies of the pathophysiology of child and adolescent psychiatric disorders--promises and limitations.

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4.  Cellular connectomes as arbiters of local circuit models in the cerebral cortex.

Authors:  Emmanuel Klinger; Alessandro Motta; Carsten Marr; Fabian J Theis; Moritz Helmstaedter
Journal:  Nat Commun       Date:  2021-05-13       Impact factor: 14.919

5.  An Introduction to Programming for Bioscientists: A Python-Based Primer.

Authors:  Berk Ekmekci; Charles E McAnany; Cameron Mura
Journal:  PLoS Comput Biol       Date:  2016-06-07       Impact factor: 4.475

Review 6.  The antipsychotic landscape: dopamine and beyond.

Authors:  Paul D Morrison; Robin M Murray
Journal:  Ther Adv Psychopharmacol       Date:  2018-01-23

7.  Quantification of neuronal density across cortical depth using automated 3D analysis of confocal image stacks.

Authors:  Jenna G Kelly; Michael J Hawken
Journal:  Brain Struct Funct       Date:  2017-02-27       Impact factor: 3.270

8.  LCN: a random graph mixture model for community detection in functional brain networks.

Authors:  Christopher Bryant; Hongtu Zhu; Mihye Ahn; Joseph Ibrahim
Journal:  Stat Interface       Date:  2017       Impact factor: 0.582

Review 9.  Disorders of the enteric nervous system - a holistic view.

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Journal:  Nat Rev Gastroenterol Hepatol       Date:  2021-01-29       Impact factor: 46.802

10.  Processing Time Reduction: an Application in Living Human High-Resolution Diffusion Magnetic Resonance Imaging Data.

Authors:  Nicolás F Lori; Augustin Ibañez; Rui Lavrador; Lucia Fonseca; Carlos Santos; Rui Travasso; Artur Pereira; Rosaldo Rossetti; Nuno Sousa; Victor Alves
Journal:  J Med Syst       Date:  2016-09-29       Impact factor: 4.460

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